install error on oracle rstudio server xml load

[genghiskhanofnz]

Hi, I have setup an Oracle RStudio Server yesterday to have this covid19.analytics package accessible anywhere anytime on web.
Sadly, other such as EpiEstim and other packages installed smoothly but failed multiple times in your package with the following error.

• installing source package ‘covid19.analytics’ ...
  ** package ‘covid19.analytics’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
  Execution halted
  ERROR: lazy loading failed for package ‘covid19.analytics’
• removing ‘/usr/local/lib/R/site-library/covid19.analytics’
  Warning in install.packages :
  installation of package ‘covid19.analytics’ had non-zero exit status

Please advise how to solve.
Thank you very much.

[mponce0]

Thanks for reporting this.
From the error message it appears to be an issue wth one of covid19.analytics dependencies: the XML package.
In particular not being able to find the libmxl2.so.2 library.

My first suggestion would be to try to install the XML package but I imagine you would find a similar problem there.

So it may be a dependency related to your particular configuration, see for instance,

https://community.rstudio.com/t/can-not-install-xml-package/48854

[genghiskhanofnz]

I was blown away by your very quick response.
I did install XML 3.99 and xml2 1.3.2 = today both installed twice
Then I tried devtools version as follows: = but still the same
My issue = I report covid data update to the Grand Round on every Wednesday and need to access your package since I am travelling many places and not at work.
Any follow-up advice will be really appreciated.

devtools::install_github("mponce0/covid19.analytics")
Downloading GitHub repo mponce0/covid19.analytics@HEAD
✓ checking for file ‘/tmp/Rtmp1ZsEQI/remotes95375035ae4/mponce0-covid19.analytics-ef3236c/DESCRIPTION’ ...
─ preparing ‘covid19.analytics’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘covid19.analytics_2.1.3.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)

• installing source package ‘covid19.analytics’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
  Execution halted
  ERROR: lazy loading failed for package ‘covid19.analytics’
• removing ‘/usr/local/lib/R/site-library/covid19.analytics’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/Rtmp1ZsEQI/file9536f8b800c/covid19.analytics_2.1.3.tar.gz’ had non-zero exit status

[genghiskhanofnz]

Can I have a patch to make it work? Thanks.

[mponce0]

OK, I see. I'm still unsure whether this is an issue with covid19.analytics or xml.
One more thing that I may ask you to try, could you try loading the XML package from one interactive R session and run one of their demos.
I tell you why: the XML package would install assuming or looking for system related libraries, such as, libxml2.
And sometimes depending on the actual system this can fail. Hence why trying to load the package would be the way to test this.
So you need to install the libxml2 library at system level and then the XML package in R.

Other than that, at the moment I can't really think of anything else as I haven't seen this error myself even when working in different systems.

Actually, now I'm a little bit puzzle... as far as I can recall covid19.analytics does not require XML.

Would you mind telling me which OS and R version are you using?

[genghiskhanofnz]

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] EpiEstim_2.2-4 ggpubr_0.4.0 ggplot2_3.3.5 dplyr_1.0.7 ggsci_2.9 scales_1.1.1

loaded via a namespace (and not attached):
[1] pkgload_1.2.3 tidyr_1.1.4 splines_4.1.1 carData_3.0-4 cellranger_1.1.0
[6] remotes_2.4.1 sessioninfo_1.1.1 pillar_1.6.4 backports_1.3.0 lattice_0.20-44
[11] quantreg_5.86 glue_1.4.2 ggsignif_0.6.3 colorspace_2.0-2 Matrix_1.3-4
[16] plyr_1.8.6 conquer_1.0.2 pkgconfig_2.0.3 devtools_2.4.2 broom_0.7.9
[21] SparseM_1.81 haven_2.4.3 purrr_0.3.4 coarseDataTools_0.6-5 processx_3.5.2
[26] incidence_1.7.3 openxlsx_4.2.4 rio_0.5.27 MatrixModels_0.5-0 tibble_3.1.5
[31] generics_0.1.1 car_3.0-11 usethis_2.1.3 ellipsis_0.3.2 cachem_1.0.6
[36] withr_2.4.2 cli_3.1.0 survival_3.2-11 magrittr_2.0.1 crayon_1.4.1
[41] readxl_1.3.1 memoise_2.0.0 mcmc_0.9-7 ps_1.6.0 fs_1.5.0
[46] fansi_0.5.0 MASS_7.3-54 rstatix_0.7.0 forcats_0.5.1 foreign_0.8-81
[51] pkgbuild_1.2.0 tools_4.1.1 fitdistrplus_1.1-6 data.table_1.14.2 prettyunits_1.1.1
[56] hms_1.1.1 lifecycle_1.0.1 matrixStats_0.61.0 stringr_1.4.0 MCMCpack_1.6-0
[61] munsell_0.5.0 zip_2.2.0 callr_3.7.0 compiler_4.1.1 rlang_0.4.12
[66] grid_4.1.1 rstudioapi_0.13 testthat_3.1.0 gtable_0.3.0 abind_1.4-5
[71] curl_4.3.2 reshape2_1.4.4 R6_2.5.1 gridExtra_2.3 fastmap_1.1.0
[76] utf8_1.2.2 rprojroot_2.0.2 desc_1.4.0 stringi_1.7.5 Rcpp_1.0.7
[81] vctrs_0.3.8 tidyselect_1.1.1 coda_0.19-4

[genghiskhanofnz]

Hi, you are very intelligent.
As you advise, I load XML = failed = see here

library(XML)
Error: package or namespace load failed for ‘XML’:
.onLoad failed in loadNamespace() for 'XML', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
libxml2.so.2: cannot open shared object file: No such file or directory

[genghiskhanofnz]

Hi = the same to xml2 = failed

library(xml2)
Error: package or namespace load failed for ‘xml2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/xml2/libs/xml2.so':
libxml2.so.2: cannot open shared object file: No such file or directory

[mponce0]

OK, so I think the issue is the xml system libraries
Can you try the following?
sudo apt install libxml2-dev
(this will install the development version which brings along headers, etc.)
Then you will need to reinstall XML from within R.

XML packages and sometime the system libraries have some reputation of being "tricky", see
https://stackoverflow.com/questions/63084235/xml-installation-seems-to-be-failing-and-not-load-on-r
https://support.bioconductor.org/p/131866/
https://community.rstudio.com/t/xml-install-complete-novice/74728/5
r-lib/actions#559

Alternatively you could try to install covid19.analytics from source, e.g.
install.packages("covid19.analytics", type="source")

[genghiskhanofnz]

@mponce0 = tried source = failed

see here.

install.packages("covid19.analytics", type="source")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-10-29/src/contrib/covid19.analytics_2.1.1.tar.gz'
Content type 'binary/octet-stream' length 3766534 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

• installing source package ‘covid19.analytics’ ...
  ** package ‘covid19.analytics’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
  Execution halted
  ERROR: lazy loading failed for package ‘covid19.analytics’
• removing ‘/usr/local/lib/R/site-library/covid19.analytics’
  Warning in install.packages :
  installation of package ‘covid19.analytics’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmp1ZsEQI/downloaded_packages’

[genghiskhanofnz]

@mponce0 = your package is my lifeline to report to the Grand Round
I have been using your package for covid reporting for the last 3 years = acknowledged your package in every presentation and thank you very much for developing such a brilliant one.
Another one = EpiEstim to calculate Re = I have regular email contacts with its developers
Thanks to both packages.

[mponce0]

Nop, it is not doing the compilation... you can see that when it states

** byte-compile and prepare package for lazy loading

BTW which repo are you using?
Can you try "0-Cloud [https]"

Alternatively, you can do the following:
install.packages("https://cran.r-project.org/src/contrib/covid19.analytics_2.1.3.tar.gz", repo=NULL, type="source")

[genghiskhanofnz]

Tried from your advice via http.

install.packages("https://cran.r-project.org/src/contrib/covid19.analytics_2.1.3.tar.gz", repo=NULL, type="source")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/covid19.analytics_2.1.3.tar.gz'
Content type 'application/x-gzip' length 3758229 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

• installing source package ‘covid19.analytics’ ...
  ** package ‘covid19.analytics’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
  Execution halted
  ERROR: lazy loading failed for package ‘covid19.analytics’
• removing ‘/usr/local/lib/R/site-library/covid19.analytics’
  Warning in install.packages :
  installation of package ‘/tmp/Rtmp1ZsEQI/downloaded_packages/covid19.analytics_2.1.3.tar.gz’ had non-zero exit status
  Warning message:
  In download.file(.rs.completeUrl(.rs.appendSlashIfNeeded(url), "src/contrib/PACKAGES.gz"), :
  URL '0-Cloud [https]/src/contrib/PACKAGES.gz': status was 'URL using bad/illegal format or missing URL'

It failed.

It also said = illegal URL 0-Cloud [https] = why?

Thanks.

[genghiskhanofnz]

@mponce0 = my home pc windows system rtools42 has libxml2
Wondering what your thoughts on whether linux system needs rtools or not.
Thanks.

[mponce0]

rtools is needed on Windows systems as they usually don't bring along compilers but I don't think they will help much in your case. Although you may want to try...

Focusing on the ubuntu system, did you install libxml2-dev using

sudo apt install libxml2-dev

After this you want to launch R, and do the following:

# remove XML
remove.packages("XML")
# reinstall XML
remove.packages("XML")

try to load XML and see what the error says.

The "0-Cloud" repository is one of the options, the first one, offered when you interactively run "install.packages(...)"

BTW I just noticed that the installation is referring to the "/usr/local/lib/R/site-library/..." this is usually a system path, ie. unless you are dong the installation as root it may not have permissions to write to it.
I'd instead recommend doing it a your own user in a "personal" library.

[genghiskhanofnz]

Yes, I will try all you advise above.
Need to create a personal library first.
Then all will follow.
Thanks.
Have a nice evening.

[genghiskhanofnz]

Hi Sir, I still can't solve this package install.
I pasted the RStudio console output and errors = finding XML.SO
I had no problems of installing your package on Windows machine at work and home.
Please confirm that your package uised XML resources from the operating system.
Thanks.
Merry Christmas.

one thing = our state has around 30K new cases and 100 deaths every week.
your package is critical for analysing this.

install.packages('XML')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-10-29/src/contrib/XML_3.99-0.8.tar.gz'
Content type 'binary/octet-stream' length 1928791 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

• installing binary package ‘XML’ ...
• DONE (XML)

The downloaded source packages are in
‘/tmp/RtmpphvzUx/downloaded_packages’
Warning message:
In grSoftVersion() :
unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
libXt.so.6: cannot open shared object file: No such file or directory

install.packages("xml2")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-10-29/src/contrib/xml2_1.3.2.tar.gz'
Content type 'binary/octet-stream' length 617914 bytes (603 KB)
==================================================
downloaded 603 KB

• installing binary package ‘xml2’ ...
• DONE (xml2)

The downloaded source packages are in
‘/tmp/RtmpphvzUx/downloaded_packages’

install.packages("covid19.analytics", type="source")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-10-29/src/contrib/covid19.analytics_2.1.1.tar.gz'
Content type 'binary/octet-stream' length 3766534 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

• installing source package ‘covid19.analytics’ ...
  ** package ‘covid19.analytics’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: .onLoad failed in loadNamespace() for 'XML', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
  libxml2.so.2: cannot open shared object file: No such file or directory
  Execution halted
  ERROR: lazy loading failed for package ‘covid19.analytics’
• removing ‘/usr/local/lib/R/site-library/covid19.analytics’
  Warning in install.packages :
  installation of package ‘covid19.analytics’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpphvzUx/downloaded_packages’

library(EpiEstim)
library(covid19.analytics)
Error in library(covid19.analytics) :
there is no package called ‘covid19.analytics’
In addition: Warning message:
In grSoftVersion() :
unable to load shared object '/usr/local/lib/R/modules//R_X11.so':
libXt.so.6: cannot open shared object file: No such file or directory
library(XML)
Error: package or namespace load failed for ‘XML’:
.onLoad failed in loadNamespace() for 'XML', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
libxml2.so.2: cannot open shared object file: No such file or directory
install.packages('XML')
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/2021-10-29/src/contrib/XML_3.99-0.8.tar.gz'
Content type 'binary/octet-stream' length 1928791 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

• installing binary package ‘XML’ ...
• DONE (XML)

The downloaded source packages are in
‘/tmp/Rtmpxib1yP/downloaded_packages’

library(XML)
Error: package or namespace load failed for ‘XML’:
.onLoad failed in loadNamespace() for 'XML', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/usr/local/lib/R/site-library/XML/libs/XML.so':
libxml2.so.2: cannot open shared object file: No such file or directory

[mponce0]

OK, I'm seeing a new type of problem here pointing to the lack of X11.
I imagine you are using MacOS in this case, correct?

Then you also need to install XQuartz -- https://www.xquartz.org -- this is a program that provides support for graphics in linux-type of OSes.

Please install XQuartz, you may need to reboot your system, then reinstall both the XML and covid19.analytics packages.

[genghiskhanofnz]

Thanks for your kind advice. I am not using MacOS though.
I will try.
Merry Christmas.